# R script for Peak Model
#  -- generated by MACS
p <- c(0.022537434466,0.0263645459791,0.0303404896066,0.0345928357323,0.0382285916697,0.0383349003229,0.0388664435886,0.0389514905111,0.0389089670498,0.0395255572381,0.0401634091569,0.0402271943488,0.0402271943488,0.0396318658912,0.0398444831975,0.0400571005038,0.0400783622344,0.0398019597362,0.0392278930093,0.0391003226255,0.0389727522417,0.0389727522417,0.0390790608949,0.0393129399318,0.0389089670498,0.0387176114742,0.0385475176292,0.0380584978247,0.038611302821,0.0384837324373,0.0383774237841,0.0382073299391,0.0374419076365,0.0376332632121,0.0378458805184,0.0386750880129,0.0387176114742,0.038845181858,0.0389514905111,0.0391003226255,0.0400145770425,0.0403972881938,0.0412052339577,0.0412902808802,0.0413328043415,0.0407162141533,0.0406099055001,0.0412902808802,0.0413115426108,0.0411627104964,0.0406099055001,0.0404185499245,0.0403547647326,0.0394405103156,0.0401208856957,0.0402484560794,0.0395042955074,0.039015275703,0.038611302821,0.0387176114742,0.0383349003229,0.038845181858,0.0387176114742,0.0397806980056,0.0393342016624,0.0394617720462,0.0402271943488,0.0407374758839,0.0409075697289,0.0404185499245,0.0402697178101,0.0393129399318,0.0389514905111,0.0382498534004,0.0383986855148,0.0380797595553,0.0381648064779,0.0379521891716,0.0377183101347,0.0383986855148,0.0385262558985,0.039185369548,0.0399933153119,0.040673690692,0.0405673820389,0.0409075697289,0.0406524289614,0.0409075697289,0.0410989253046,0.0406099055001,0.0410776635739,0.0412264956883,0.040673690692,0.0404185499245,0.0400145770425,0.0399082683894,0.0395680806993,0.0396531276218,0.0398870066587,0.0401421474263,0.0394405103156,0.0387601349354,0.0393767251237,0.0390790608949,0.03958934243,0.0392704164705,0.0397806980056,0.0396318658912,0.03958934243,0.0391641078174,0.0397806980056,0.0404185499245,0.0404610733857,0.0409075697289,0.0410564018433,0.0416729920315,0.0418005624153,0.0418430858766,0.0418856093378,0.0422895822198,0.042162011836,0.0421832735666,0.0414816364559,0.0413328043415,0.0409926166514,0.0407374758839,0.0406099055001,0.0404398116551,0.040503596847,0.0403547647326,0.0402697178101,0.0403335030019,0.0402484560794,0.0402697178101,0.0401208856957,0.0399720535813,0.0400783622344,0.0396106041606,0.0392704164705,0.0393129399318,0.0393342016624,0.0390577991642,0.0396956510831,0.0398444831975,0.0399507918506,0.0405673820389,0.0408225228064,0.0411201870352,0.0417367772234,0.0419068710684,0.0419706562603,0.0419706562603,0.0418643476072,0.0422683204891,0.0426085081792,0.0423108439504,0.0419706562603,0.0420557031828,0.0407799993451,0.040673690692,0.0404398116551,0.0407374758839,0.0403972881938,0.0401634091569,0.0403335030019,0.0403122412713,0.0404398116551,0.0407374758839,0.0422045352972,0.0425234612567,0.0431613131755,0.0427148168323,0.0434377156737,0.0431400514449,0.0432676218287,0.0431825749061,0.0431613131755,0.0430337427917,0.042332105681,0.0418856093378,0.0416942537622,0.0415666833784,0.0412264956883,0.0413540660721,0.0414603747252,0.0415241599171,0.0414603747252,0.0414816364559,0.0415666833784,0.0416729920315,0.0416517303009,0.0416729920315,0.041587945109,0.0418430858766,0.0409075697289,0.0410351401127,0.0418856093378,0.0419493945297,0.0424171526035,0.0427786020242,0.0425447229873,0.0430550045224,0.043076266253,0.0426722933711,0.0433314070205,0.04365033298,0.0431400514449,0.0434164539431,0.04365033298,0.0438629502862,0.0442243997069,0.0448622516258,0.0449260368177,0.0450110837402,0.0448197281645,0.0446071108582,0.044564587397,0.0443519700907,0.0445433256664,0.044394493552,0.0447559429726,0.0436078095187,0.043820426825,0.0441180910538,0.0441180910538,0.0441180910538,0.0444582787438,0.0449260368177,0.0446496343195,0.0444582787438,0.0445220639357,0.0458615529653,0.0459891233491,0.0464994048842,0.046967162958,0.0473498741093,0.0468608543048,0.0468395925742,0.0465419283454,0.0466057135373,0.0469884246886,0.0464781431535,0.0464143579616,0.0463718345004,0.0462867875779,0.0462867875779,0.0469246394967,0.047137256803,0.0474987062237,0.048625577947,0.0482853902569,0.0482003433344,0.0487106248695,0.0487106248695,0.0494973089028,0.0499438052459,0.0503690398585,0.0508367979323,0.0514321263899,0.0503903015891,0.050454086781,0.051028153508,0.0511132004305,0.0515809585043,0.0515384350431,0.0515384350431,0.0516872671575,0.0512620325449,0.0507517510098,0.0514746498512,0.0517935758106,0.0520061931169,0.0523889042682,0.0519849313863,0.0518786227331,0.0518786227331,0.0518573610025,0.052346380807,0.0531968500321,0.052856662342,0.053600822914,0.0538559636816,0.0542599365635,0.0551741909805,0.0557269959769,0.056003398475,0.0559183515525,0.0563223244344,0.056577465202,0.057151531929,0.0571940553902,0.0571940553902,0.0567262973164,0.0568751294308,0.0568326059695,0.0567900825083,0.057321625774,0.0572365788515,0.0571727936596,0.0579169542316,0.0574704578884,0.0575342430803,0.0581720949991,0.0582146184604,0.0588949938405,0.0591076111468,0.0599580803719,0.0605321470989,0.0610211669033,0.0611487372871,0.0620842534347,0.0628496757373,0.0638064536156,0.064125379575,0.06435925861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m <- 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ycorr <- 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altd  <- c(141)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('19-LFY-GSE24568/lfy-samp-rep2-GSM605657/all.1x36mers.TAIR10.unique.MACS2_model.pdf',height=6,width=6)
plot(x,p,type='l',col=c('red'),main='Peak Model',xlab='Distance to the middle',ylab='Percentage')
lines(x,m,col=c('blue'))
legend('topleft',c('forward tags','reverse tags'),lty=c(1,1,1),col=c('red','blue'))
plot(xcorr,ycorr,type='l',col=c('black'),main='Cross-Correlation',xlab='Lag between + and - tags',ylab='Correlation')
abline(v=altd,lty=2,col=c('red'))
legend('topleft','alternative lag(s)',lty=2,col='red')
legend('right','alt lag(s) : 141',bty='n')
dev.off()